RetrogeneDB ID: retro_hsap_3873

Retrocopy location

• Organism: Human (Homo sapiens)
• Coordinates: 7:76744718..76745204(-)
• Located in intron of: ENSG00000259628

Retrocopy information

• Ensembl ID: ENSG00000213542
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: RPL7A
• Ensembl ID: ENSG00000260501
• Aliases: None
• Description: ribosomal protein L7a [Source:HGNC Symbol;Acc:10364]

Sequence

>retro_hsap_3873
CAGACCAGAGACAAAGCAAGAGAAGAAGTGGAGGCTGTTGGCCCAGGCAGAGTTGTGGGCAAAGGGGACCTCCCCATGAA
GAGACTACCTGTCTTTCGAGCAGGAGTTAACACCGTCACCACCTTTGTGGATAACAAGAAAGCTCCGCTGGTGGTGACTA
CACACGACATGGATCCCATTGAGCTGACTGTTTTCCTGCCTGTCCTGTGTCATAAAATGGGGGCCACTTGCTGCATTATC
AAGGGGAAGGCAAGACTGGGATGTCTAGTTCACAGGAAGACCTACACCACTGTCGACTTCACACAGGTTAACTCAGAAGA
CAAAGGAGCTTTGGCTAAGCTGGTGGAAGCTATCGGGACCAATTACAATGCCAGATACGATGAGACCCACTGTCACTGGG
ACGGCAATGTCCTGGGTCCCAAGTCTGTGGCTCACATTGCCAAGCTCGAAAAGGCAAAGGCTAAAGAACTTGCCACTAAA
CTGGGT

Alignment

ORF - retro_hsap_3873 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 73.46 %
• Parental protein coverage: 60.9 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  ETKQEKKQRLLARAEKKAAGKGDVPTKRPPVLRAGVNTVTTLVENKKAQLVVIAHDVDPIELVVFLPALC
          .T.........A.......GKGD.P.KR.PV.RAGVNTVTT.V.NKKA.LVV..HD.DPIEL.VFLP.LC
Retrocopy QTRDKAREEVEAVGPGRVVGKGDLPMKRLPVFRAGVNTVTTFVDNKKAPLVVTTHDMDPIELTVFLPVLC

Parental  RKMGVPYCIIKGKARLGRLVHRKTCTTVAFTQVNSEDKGALAKLVEAIRTNYNDRYDEIRRHWGGNVLGP
          .KMG...CIIKGKARLG.LVHRKT.TTV.FTQVNSEDKGALAKLVEAI.TNYN.RYDE...HW.GNVLGP
Retrocopy HKMGATCCIIKGKARLGCLVHRKTYTTVDFTQVNSEDKGALAKLVEAIGTNYNARYDETHCHWDGNVLGP

Parental  KSVARIAKLEKAKAKELATKLG
          KSVA.IAKLEKAKAKELATKLG
Retrocopy KSVAHIAKLEKAKAKELATKLG

Legend:

• *: Stop codon
• >: Forward frameshift by one nucleotide
• <: Reverse frameshift by one nucleotide

Expression

RNA-Seq

Expression validation based on RNA-Seq data:

Library	Retrocopy expression	Parental gene expression
bodymap2_adipose	0.08 RPM	0.00 RPM
bodymap2_adrenal	0.12 RPM	0.00 RPM
bodymap2_brain	0.02 RPM	0.00 RPM
bodymap2_breast	0.23 RPM	0.00 RPM
bodymap2_colon	0.02 RPM	0.00 RPM
bodymap2_heart	0.06 RPM	0.00 RPM
bodymap2_kidney	0.08 RPM	0.00 RPM
bodymap2_liver	0.06 RPM	0.00 RPM
bodymap2_lung	0.14 RPM	0.00 RPM
bodymap2_lymph_node	0.37 RPM	0.00 RPM
bodymap2_ovary	0.04 RPM	0.00 RPM
bodymap2_prostate	0.09 RPM	0.00 RPM
bodymap2_skeletal_muscle	0.00 RPM	0.00 RPM
bodymap2_testis	0.08 RPM	0.00 RPM
bodymap2_thyroid	0.06 RPM	0.00 RPM
bodymap2_white_blood_cells	0.00 RPM	0.00 RPM

ChIP-Seq

RNA Polymerase II actvity near the 5' end of retro_hsap_3873 was not detected

EST

No EST(s) were mapped for retro_hsap_3873 retrocopy.

TSS

No TSS is located nearby retro_hsap_3873 retrocopy 5' end.

Lab

retro_hsap_3873 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_hsap_3873 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 1 parental gene, and 36 retrocopies.

Species	Parental gene accession	Retrocopies number
Homo sapiens	ENSG00000260501	36 retrocopies	retro_hsap_1031, retro_hsap_1103, retro_hsap_1157, retro_hsap_1327, retro_hsap_1340, retro_hsap_1402, retro_hsap_1435, retro_hsap_1565, retro_hsap_1656, retro_hsap_1936, retro_hsap_1937, retro_hsap_2016, retro_hsap_2172, retro_hsap_218, retro_hsap_2476, retro_hsap_261, retro_hsap_2697, retro_hsap_2806, retro_hsap_2893, retro_hsap_2931, retro_hsap_297, retro_hsap_3060, retro_hsap_3572, retro_hsap_3603, retro_hsap_3749, retro_hsap_3766, retro_hsap_377, retro_hsap_3873 , retro_hsap_3877, retro_hsap_4135, retro_hsap_4141, retro_hsap_612, retro_hsap_660, retro_hsap_750, retro_hsap_767, retro_hsap_771,

Population studies

Expression level across human populations :

Library	Retrogene expression
CEU_NA11831	0.11 RPM
CEU_NA11843	0.23 RPM
CEU_NA11930	0.33 RPM
CEU_NA12004	0.38 RPM
CEU_NA12400	0.28 RPM
CEU_NA12751	0.15 RPM
CEU_NA12760	0.13 RPM
CEU_NA12827	0.14 RPM
CEU_NA12872	0.22 RPM
CEU_NA12873	0.16 RPM
FIN_HG00183	0.25 RPM
FIN_HG00277	0.41 RPM
FIN_HG00315	0.17 RPM
FIN_HG00321	0.30 RPM
FIN_HG00328	0.14 RPM
FIN_HG00338	0.26 RPM
FIN_HG00349	0.17 RPM
FIN_HG00375	0.15 RPM
FIN_HG00377	0.20 RPM
FIN_HG00378	0.11 RPM
GBR_HG00099	0.09 RPM
GBR_HG00111	0.37 RPM
GBR_HG00114	0.24 RPM
GBR_HG00119	0.26 RPM
GBR_HG00131	0.29 RPM
GBR_HG00133	0.43 RPM
GBR_HG00134	0.31 RPM
GBR_HG00137	0.27 RPM
GBR_HG00142	0.47 RPM
GBR_HG00143	0.29 RPM
TSI_NA20512	0.11 RPM
TSI_NA20513	0.24 RPM
TSI_NA20518	0.17 RPM
TSI_NA20532	0.34 RPM
TSI_NA20538	0.05 RPM
TSI_NA20756	0.09 RPM
TSI_NA20765	0.21 RPM
TSI_NA20771	0.17 RPM
TSI_NA20786	0.05 RPM
TSI_NA20798	0.19 RPM
YRI_NA18870	0.10 RPM
YRI_NA18907	0.00 RPM
YRI_NA18916	0.13 RPM
YRI_NA19093	0.08 RPM
YRI_NA19099	0.13 RPM
YRI_NA19114	0.05 RPM
YRI_NA19118	0.21 RPM
YRI_NA19213	0.14 RPM
YRI_NA19214	0.05 RPM
YRI_NA19223	0.18 RPM

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Indel association:

No indels were associated with its genomic coordinates. Based on Kabza et al. 2015 (PubMed).